Abstract
Constructivist biosemiotics foundations (CBF) imply the first-person basis of cognition. CBF are developed by the biology of cognition, relational biology, enactive approach, ecology of mind, second order cybernetics, genetic epistemology, gestalt, ecological perception and affordances, and active inference by minimization of free energy. CBF reject the idea of an objective independent reality to be represented (cognitivism) by information processing (computationalism) in order to be the fittest (adaptationism). CBF assumes that perception is the behavioral configuration of an object and objects are tokens for eigen-behaviors. Cognition takes place in the organism-environment structural coupling during the ontogeny and phylogeny of all biological unities including unicellular organisms. Therefore, if exogenous DNA particles (virus or trans-sequence) are just tokens for the cell signalling eigen-behaviors, if there is no ‘information’ in the DNA sequence, how can we explain that the same virus or trans- sequence is associated with a similar phenotype? We call this ‘exogenomic problem’. With this basic example, but sufficiently generic to the whole biological world, we agree respectively with Autopoiesis, (Metabolism, Repair)-system, and Gaia theory: i) ‘Information, code and meaning’ in the DNA sequence belong to the domain of the observer’s description. ii) Genetic ‘information’ is not a program or algorithmic software in DNA sequence. Rather it is a microphysical observable mode of eigen-behaviors in biological unities. iii) The transfer and acquisition of DNA particles is a biospheric phenomenon that maintains its homeorhesis, symbiotic and biosemiotic entailment. Based on the theoretical and experimental results of these theories, it is concluded that genetic ‘information’ is not a genomic sequence, nor any kind of information (algorithmic or semantic), but for the cell DNA must embody physical forcing. Genetic characters are the effects and not the cause of phenotype and DNA particles do not ‘use or manipulate’ cellular metabolism. Rather, any cellular configuration change that occurred before or during DNA perturbation (coincident or not with the observation of certain phenotype) is determined on the basis of the cellular standpoint.
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Notes
The nature of the phenomenon of life can be explained, among other important characterizations, as a physical realization of the (Metabolism, Repair)-system, Autopoiesis or Gaia. While Autopoesis is a descriptive and generative process of the living, (M,R)-system presents a series of more rigorous formal explanatory propositions. Both, (M,R)-system and Autopoiesis are equivalent models of organisms at cellular scale (Zaretzky and Letelier 2002, Letelier et al. 2003) whereas Gaia exists at the planetary scale. Accordingly, (M,R)- Autopoiesis of the biosphere as a unity is biologically Gaia (Margulis and Sagan 1986; Mikulecky 2000). Although biological unities produce themselves autonomously from the milieu interior (Bernard 1878), no organism is capable to be alive in a non-biological environment. In other words, to be realized the living process unambiguously needs a ‘self-centered world’ = umwelt (von Uexküll 1909), which can be equivalent to Gaia theory = bio habitable environment by and for the biosphere (Lovelock and Margulis 1974). That is to say, the milieu interior-umwelt structural coupling or shortly (M, R)-Gaia Autopoiesis is sine qua non for the living individuation. The individuation of (M, R)-Gaia Autopoiesis may be seen as the ‘pattern which connects’ the biological world and their multiplicity of metabolic events, scales and distinctions.
The reason why organisms are called unities instead of wholes is that the assumption of a whole presupposes the assumption of parts, which leads to a mechanistic (fractionable) view of life. The phrase ‘the whole is more than the sum of its parts’ indicates that the synthesis of the biological unity is inverse to the analysis of its parts (Rosen 1998). This is a very Kantian approach to a biological being. The enterprise of molecular, system, synthetic, and computational biology looks for the ‘exact connections’ to resynthesize (self-organize) a biological unity by means of analyzing the parts and its computable connections. Maturana and Rosen take distance to this Kantian approach. While Rosen calls a biological being a (M,R)-system which is non-fractionable, thus non-computable (Rosen 1998), Maturana calls an autopoietic unity in distinction with unit (Maturana 1979). Unit refers to inert particles. A virus can be a unit, but a cell is a unity because of its invariant (M,R)-autopoiesis, which, likewise, is a description that differs from the idea of self-organization (Maturana 2002). I emphasize that ‘parts’ are parts of ‘units’ and ‘fractions’ are fractions of ‘unities’. The denotation is quite different. Parts can be analyzed in isolation from the whole (of the mechanical system), but fractions cannot be completely understood in isolation or they can display few possible detectable ‘functions’ in isolation of infinite posibilities within the biological unity.
A Mendelian factor is not a specific molecular sequence, but it refers to the ‘active site’ that is not fractionable or isolable from the system-unity. A Mendelian factor exerts physical forces within a larger system while the inertial mass of the system impresses forces over it (for details see Rosen 1994, 1998 chapter 1).
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This manuscript is dedicated to the memory of Benjamin Rothman. The anonymous reviewer and the editors are acknowledged for their invaluable contributions to the final form of the manuscript. Wallonie-Bruxelles International (IN-WBI) founds SR.
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dC Rubin, S.S. From the Cellular Standpoint: is DNA Sequence Genetic ‘Information’?. Biosemiotics 10, 247–264 (2017). https://doi.org/10.1007/s12304-017-9303-x
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DOI: https://doi.org/10.1007/s12304-017-9303-x